SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 98
Search took 0.02 seconds.
Search: Posts Made By: bastianwur
Forum: Illumina/Solexa 10-06-2016, 07:19 AM
Replies: 4
Views: 1,563
Posted By bastianwur
Yeah, that can for sure happen during the...

Yeah, that can for sure happen during the assembly processes, we've seen this during some comparative genomics tests.
But as suggested, use Pilon for error correction afterwards. It needs the reads...
Forum: RNA Sequencing 10-06-2016, 07:14 AM
Replies: 0
Views: 1,004
Posted By bastianwur
What to do if you only have a single RNAseq condition?

The setup is for sure more complicated, we sequenced more than only a single condition, but it boils down that I need to somehow do something with RNAseq reads for only a single condition.
...
Forum: RNA Sequencing 10-06-2016, 07:01 AM
Replies: 4
Views: 1,681
Posted By bastianwur
Depending on the setup, 20% might also be...

Depending on the setup, 20% might also be acceptable.

What we've seen in some of our experiments is that, although the traces don't show any big peaks, we got a half ton of eukaryotic rRNA...
Forum: Illumina/Solexa 10-06-2016, 06:54 AM
Replies: 4
Views: 1,563
Posted By bastianwur
Miscalls in Illumina sequencing are not very...

Miscalls in Illumina sequencing are not very frequent, and should probably not be a consideration at this step.
As QC measure you can use the tool pilon for error correction afterwards.


...
Forum: Bioinformatics 10-06-2016, 06:47 AM
Replies: 12
Views: 10,602
Posted By bastianwur
If you're going to merge the fastq files with a...

If you're going to merge the fastq files with a custom script: Make sure to not put read-1 and read-2 in the wrong order, else the assembler might discard them (at least IDBA_UD does; which makes...
Forum: Bioinformatics 10-06-2016, 06:41 AM
Replies: 3
Views: 1,168
Posted By bastianwur
I'd make DE all vs all, then sort out the...

I'd make DE all vs all, then sort out the statistically significant ones (no matter where they are significant) and do clustering on these (as suggested), to see which patterns are in there.

I...
Forum: General 07-20-2016, 07:59 AM
Replies: 3
Views: 1,306
Posted By bastianwur
I've for sure already cited the altschul paper...

I've for sure already cited the altschul paper ^^.
An appendix with the genomes/accession numbers sounds like a potentially good idea (although annoying) :).

But it's more about the citation. Do...
Forum: Metagenomics 07-20-2016, 07:53 AM
Replies: 3
Views: 2,981
Posted By bastianwur
Opera also scaffolds. It might be...

Opera also scaffolds.

It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the...
Forum: Metagenomics 07-20-2016, 07:47 AM
Replies: 1
Views: 1,637
Posted By bastianwur
Normally then the number of unassigned reads...

Normally then the number of unassigned reads should increase (because the assignment gets too fuzzy).
If not...where did they go to?
Forum: Metagenomics 07-20-2016, 07:42 AM
Replies: 3
Views: 2,070
Posted By bastianwur
Other things you'll need to do: - assembly,...

Other things you'll need to do:
- assembly, best cross-assembly if you have multiple samples
- genomic binning (e.g. maxBin)
- gene prediction (prodigal has a setting for meta, but only bacteria;...
Forum: Metagenomics 07-20-2016, 07:36 AM
Replies: 11
Views: 2,623
Posted By bastianwur
Not sure if I get the question....you have...

Not sure if I get the question....you have reference genomes for all the bacterial data in your sample? And that then only 1 read of the PEs map to these genomes. That's how it sounds like for me.
...
Forum: Bioinformatics 07-20-2016, 07:27 AM
Replies: 4
Views: 1,655
Posted By bastianwur
For another quick check use Kraken, which does...

For another quick check use Kraken, which does the assignment based on kmer comparison to a database.
It comes with a bacterial database, I think, and is relatively fast.
Forum: RNA Sequencing 07-20-2016, 07:22 AM
Replies: 2
Views: 1,367
Posted By bastianwur
Why would the length matter? You should be...

Why would the length matter? You should be comparing the same gene between conditions (then the length doesn't matter). Comparing different genes in the same condition (where a length correction...
Forum: Illumina/Solexa 07-20-2016, 07:16 AM
Replies: 2
Views: 1,206
Posted By bastianwur
You have the same experiment twice? To what do...

You have the same experiment twice?
To what do you want to compare it to?
Forum: General 07-20-2016, 07:11 AM
Replies: 3
Views: 1,306
Posted By bastianwur
How do I cite a custom blast database?

Hi everyone,

I have a small problem.
I'm trying to finish writing a paper, and one of the remaining questions is how to deal with custom blast databases.
e.g. a simple thing: I use the human...
Forum: Bioinformatics 01-13-2016, 06:09 AM
Replies: 218
Views: 145,257
Posted By bastianwur
I'm trying to run STAR at the moment, but it's...

I'm trying to run STAR at the moment, but it's throwing me an error while generating the genome.

I simply use the standard command:
./STAR --runMode genomeGenerate --genomeDir...
Forum: Metagenomics 06-04-2015, 07:10 AM
Replies: 5
Views: 2,618
Posted By bastianwur
Default behaviour: First it'll use the swap, and...

Default behaviour: First it'll use the swap, and if the swap gets nearly full, then the kernel will kill the program.

Do you really have only 12 GB available?

Apparently the Megahit assembler...
Forum: De novo discovery 06-04-2015, 07:03 AM
Replies: 7
Views: 4,976
Posted By bastianwur
There are tools like CGAL and RSEM-EVAL, which...

There are tools like CGAL and RSEM-EVAL, which calculate the likelyhood of the reads belonging to the actual assembly. That might help when you're having more than 1.

Since sometimes the size of...
Forum: Bioinformatics 06-04-2015, 06:57 AM
Replies: 2
Views: 1,330
Posted By bastianwur
You can try some of the tools which evaluate the...

You can try some of the tools which evaluate the quality of the mapping like CGAL or RSEM-EVAL. Maybe these can give you an idea which assembly is better.
Forum: Bioinformatics 06-04-2015, 06:52 AM
Replies: 3
Views: 1,336
Posted By bastianwur
There's no good answer for this. Besides that...

There's no good answer for this.
Besides that I'd use the p/q value from the output, that's at least easy ;).
Forum: Bioinformatics 06-04-2015, 06:46 AM
Replies: 2
Views: 861
Posted By bastianwur
I'd try to first error correct the 454, then...

I'd try to first error correct the 454, then merge everything together and run as one input.
But that's just my first reaction, and I haven't tried that before.
Forum: Bioinformatics 06-04-2015, 06:41 AM
Replies: 278
Views: 115,510
Posted By bastianwur
Contigs, or scaffolds? Have you tried giving...

Contigs, or scaffolds?
Have you tried giving the a possible distance for the reads to the assembler?
Forum: Bioinformatics 06-04-2015, 06:21 AM
Replies: 3
Views: 1,385
Posted By bastianwur
Sorry for the late answer, not regularly here. ...

Sorry for the late answer, not regularly here.
the iprlookup option will just look up if your protein has already been previously calculated at the EBI, and will return the results, which will also...
Forum: RNA Sequencing 04-21-2015, 04:49 AM
Replies: 2
Views: 1,340
Posted By bastianwur
No clue what the biological cause could be. ...

No clue what the biological cause could be.
What are your genes in this case? Protein coding sequences, or also noncoding RNA? If noncoding is included, does it also include noncoding besides tRNA...
Forum: RNA Sequencing 04-21-2015, 04:44 AM
Replies: 1
Views: 1,151
Posted By bastianwur
I don't think the differences in read length...

I don't think the differences in read length should matter too much (practical example: People do normalization with trimmed reads, they all have different lengths).
Because what you want is the...
Showing results 1 to 25 of 98

 


All times are GMT -8. The time now is 11:10 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO